This article explains how to annotate documents that have been opened in PDF Viewer directly from Safari
If you have set the PDF Viewer app has your default app for PDF documents then Safari will open PDF documents in the PDF Viewer app.
When you open a PDF document using the "Open With Preview" button in Safari, the PDF document is not saved anywhere and loaded from a temporary storage.
The annotation tool button will be greyed out and annotating the document will not be possible when you open a document in this manner. This is an expected behavior.
If you wish to annotate such a PDF document then you will have to manually download the PDF document on your computer and then open that copy of the document using PDF Viewer to annotate the document.